Job ID = 5790659 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:10:15 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 26,796,988 reads read : 53,593,976 reads written : 26,796,988 reads 0-length : 26,796,988 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:31 26796988 reads; of these: 26796988 (100.00%) were unpaired; of these: 602162 (2.25%) aligned 0 times 18966172 (70.78%) aligned exactly 1 time 7228654 (26.98%) aligned >1 times 97.75% overall alignment rate Time searching: 00:19:33 Overall time: 00:19:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 717726 / 26194826 = 0.0274 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 05:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 05:44:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:44:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:44:11: 1000000 INFO @ Wed, 22 Apr 2020 05:44:16: 2000000 INFO @ Wed, 22 Apr 2020 05:44:22: 3000000 INFO @ Wed, 22 Apr 2020 05:44:27: 4000000 INFO @ Wed, 22 Apr 2020 05:44:33: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 05:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 05:44:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:44:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:44:39: 6000000 INFO @ Wed, 22 Apr 2020 05:44:41: 1000000 INFO @ Wed, 22 Apr 2020 05:44:45: 7000000 INFO @ Wed, 22 Apr 2020 05:44:47: 2000000 INFO @ Wed, 22 Apr 2020 05:44:51: 8000000 INFO @ Wed, 22 Apr 2020 05:44:53: 3000000 INFO @ Wed, 22 Apr 2020 05:44:57: 9000000 INFO @ Wed, 22 Apr 2020 05:44:59: 4000000 INFO @ Wed, 22 Apr 2020 05:45:03: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 05:45:05: 5000000 INFO @ Wed, 22 Apr 2020 05:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 05:45:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:45:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:45:09: 11000000 INFO @ Wed, 22 Apr 2020 05:45:11: 6000000 INFO @ Wed, 22 Apr 2020 05:45:11: 1000000 INFO @ Wed, 22 Apr 2020 05:45:15: 12000000 INFO @ Wed, 22 Apr 2020 05:45:17: 7000000 INFO @ Wed, 22 Apr 2020 05:45:17: 2000000 INFO @ Wed, 22 Apr 2020 05:45:21: 13000000 INFO @ Wed, 22 Apr 2020 05:45:23: 8000000 INFO @ Wed, 22 Apr 2020 05:45:23: 3000000 INFO @ Wed, 22 Apr 2020 05:45:27: 14000000 INFO @ Wed, 22 Apr 2020 05:45:29: 9000000 INFO @ Wed, 22 Apr 2020 05:45:29: 4000000 INFO @ Wed, 22 Apr 2020 05:45:33: 15000000 INFO @ Wed, 22 Apr 2020 05:45:35: 10000000 INFO @ Wed, 22 Apr 2020 05:45:35: 5000000 INFO @ Wed, 22 Apr 2020 05:45:39: 16000000 INFO @ Wed, 22 Apr 2020 05:45:41: 11000000 INFO @ Wed, 22 Apr 2020 05:45:41: 6000000 INFO @ Wed, 22 Apr 2020 05:45:45: 17000000 INFO @ Wed, 22 Apr 2020 05:45:47: 12000000 INFO @ Wed, 22 Apr 2020 05:45:47: 7000000 INFO @ Wed, 22 Apr 2020 05:45:51: 18000000 INFO @ Wed, 22 Apr 2020 05:45:53: 13000000 INFO @ Wed, 22 Apr 2020 05:45:54: 8000000 INFO @ Wed, 22 Apr 2020 05:45:57: 19000000 INFO @ Wed, 22 Apr 2020 05:45:59: 14000000 INFO @ Wed, 22 Apr 2020 05:46:00: 9000000 INFO @ Wed, 22 Apr 2020 05:46:03: 20000000 INFO @ Wed, 22 Apr 2020 05:46:05: 15000000 INFO @ Wed, 22 Apr 2020 05:46:06: 10000000 INFO @ Wed, 22 Apr 2020 05:46:09: 21000000 INFO @ Wed, 22 Apr 2020 05:46:11: 16000000 INFO @ Wed, 22 Apr 2020 05:46:12: 11000000 INFO @ Wed, 22 Apr 2020 05:46:15: 22000000 INFO @ Wed, 22 Apr 2020 05:46:17: 17000000 INFO @ Wed, 22 Apr 2020 05:46:18: 12000000 INFO @ Wed, 22 Apr 2020 05:46:21: 23000000 INFO @ Wed, 22 Apr 2020 05:46:23: 18000000 INFO @ Wed, 22 Apr 2020 05:46:24: 13000000 INFO @ Wed, 22 Apr 2020 05:46:27: 24000000 INFO @ Wed, 22 Apr 2020 05:46:29: 19000000 INFO @ Wed, 22 Apr 2020 05:46:30: 14000000 INFO @ Wed, 22 Apr 2020 05:46:33: 25000000 INFO @ Wed, 22 Apr 2020 05:46:35: 20000000 INFO @ Wed, 22 Apr 2020 05:46:36: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 05:46:36: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 05:46:36: #1 total tags in treatment: 25477100 INFO @ Wed, 22 Apr 2020 05:46:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:46:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:46:36: 15000000 INFO @ Wed, 22 Apr 2020 05:46:36: #1 tags after filtering in treatment: 25477000 INFO @ Wed, 22 Apr 2020 05:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:46:36: #1 finished! INFO @ Wed, 22 Apr 2020 05:46:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:46:39: #2 number of paired peaks: 4473 INFO @ Wed, 22 Apr 2020 05:46:39: start model_add_line... INFO @ Wed, 22 Apr 2020 05:46:39: start X-correlation... INFO @ Wed, 22 Apr 2020 05:46:39: end of X-cor INFO @ Wed, 22 Apr 2020 05:46:39: #2 finished! INFO @ Wed, 22 Apr 2020 05:46:39: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 05:46:39: #2 alternative fragment length(s) may be 51,405,503 bps INFO @ Wed, 22 Apr 2020 05:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.05_model.r WARNING @ Wed, 22 Apr 2020 05:46:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:46:39: #2 You may need to consider one of the other alternative d(s): 51,405,503 WARNING @ Wed, 22 Apr 2020 05:46:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:46:39: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:46:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:46:41: 21000000 INFO @ Wed, 22 Apr 2020 05:46:42: 16000000 INFO @ Wed, 22 Apr 2020 05:46:47: 22000000 INFO @ Wed, 22 Apr 2020 05:46:48: 17000000 INFO @ Wed, 22 Apr 2020 05:46:52: 23000000 INFO @ Wed, 22 Apr 2020 05:46:54: 18000000 INFO @ Wed, 22 Apr 2020 05:46:58: 24000000 INFO @ Wed, 22 Apr 2020 05:47:00: 19000000 INFO @ Wed, 22 Apr 2020 05:47:04: 25000000 INFO @ Wed, 22 Apr 2020 05:47:06: 20000000 INFO @ Wed, 22 Apr 2020 05:47:07: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 05:47:07: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 05:47:07: #1 total tags in treatment: 25477100 INFO @ Wed, 22 Apr 2020 05:47:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:47:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:47:08: #1 tags after filtering in treatment: 25477000 INFO @ Wed, 22 Apr 2020 05:47:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:47:08: #1 finished! INFO @ Wed, 22 Apr 2020 05:47:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:47:10: #2 number of paired peaks: 4473 INFO @ Wed, 22 Apr 2020 05:47:10: start model_add_line... INFO @ Wed, 22 Apr 2020 05:47:10: start X-correlation... INFO @ Wed, 22 Apr 2020 05:47:10: end of X-cor INFO @ Wed, 22 Apr 2020 05:47:10: #2 finished! INFO @ Wed, 22 Apr 2020 05:47:10: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 05:47:10: #2 alternative fragment length(s) may be 51,405,503 bps INFO @ Wed, 22 Apr 2020 05:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.10_model.r WARNING @ Wed, 22 Apr 2020 05:47:10: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:47:10: #2 You may need to consider one of the other alternative d(s): 51,405,503 WARNING @ Wed, 22 Apr 2020 05:47:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:47:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:47:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:47:12: 21000000 INFO @ Wed, 22 Apr 2020 05:47:18: 22000000 INFO @ Wed, 22 Apr 2020 05:47:23: 23000000 INFO @ Wed, 22 Apr 2020 05:47:29: 24000000 INFO @ Wed, 22 Apr 2020 05:47:34: 25000000 INFO @ Wed, 22 Apr 2020 05:47:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:47:37: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 05:47:37: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 05:47:37: #1 total tags in treatment: 25477100 INFO @ Wed, 22 Apr 2020 05:47:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:47:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:47:38: #1 tags after filtering in treatment: 25477000 INFO @ Wed, 22 Apr 2020 05:47:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:47:38: #1 finished! INFO @ Wed, 22 Apr 2020 05:47:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:47:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:47:40: #2 number of paired peaks: 4473 INFO @ Wed, 22 Apr 2020 05:47:40: start model_add_line... INFO @ Wed, 22 Apr 2020 05:47:40: start X-correlation... INFO @ Wed, 22 Apr 2020 05:47:40: end of X-cor INFO @ Wed, 22 Apr 2020 05:47:40: #2 finished! INFO @ Wed, 22 Apr 2020 05:47:40: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 05:47:40: #2 alternative fragment length(s) may be 51,405,503 bps INFO @ Wed, 22 Apr 2020 05:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.20_model.r WARNING @ Wed, 22 Apr 2020 05:47:40: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:47:40: #2 You may need to consider one of the other alternative d(s): 51,405,503 WARNING @ Wed, 22 Apr 2020 05:47:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:47:40: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.05_summits.bed INFO @ Wed, 22 Apr 2020 05:48:05: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1495 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:48:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:48:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:48:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:48:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.10_summits.bed INFO @ Wed, 22 Apr 2020 05:48:37: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (923 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:48:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433270/SRX5433270.20_summits.bed INFO @ Wed, 22 Apr 2020 05:49:07: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。